Author: bugman
Date: Sun Nov 17 13:42:30 2013
New Revision: 21480
URL: http://svn.gna.org/viewcvs/relax?rev=21480&view=rev
Log:
Added the 'TAP03' R2eff calculating function to the relax library.
This is the Trott, Abergel and Palmer 2003 R1rho analytic model for 2-site
off-resonance exchange.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.
Added:
branches/relax_disp/lib/dispersion/tap03.py
- copied, changed from r21474,
branches/relax_disp/lib/dispersion/mp05.py
Modified:
branches/relax_disp/lib/dispersion/__init__.py
Modified: branches/relax_disp/lib/dispersion/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/__init__.py?rev=21480&r1=21479&r2=21480&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/__init__.py (original)
+++ branches/relax_disp/lib/dispersion/__init__.py Sun Nov 17 13:42:30 2013
@@ -38,6 +38,7 @@
'ns_cpmg_2site_star',
'ns_r1rho_2site',
'ns_matrices',
+ 'tap03',
'tp02',
'tsmfk01',
'two_point'
Copied: branches/relax_disp/lib/dispersion/tap03.py (from r21474,
branches/relax_disp/lib/dispersion/mp05.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/tap03.py?p2=branches/relax_disp/lib/dispersion/tap03.py&p1=branches/relax_disp/lib/dispersion/mp05.py&r1=21474&r2=21480&rev=21480&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/mp05.py (original)
+++ branches/relax_disp/lib/dispersion/tap03.py Sun Nov 17 13:42:30 2013
@@ -22,13 +22,13 @@
###############################################################################
# Module docstring.
-"""This Miloushev and Palmer (2005) 2-site exchange R1rho model.
+"""This is the Trott, Abergel and Palmer (2003) off-resonance 2-site
exchange R1rho model.
-This module is for the function, gradient and Hessian of the MP05 model.
The model is named after the reference:
+This module is for the function, gradient and Hessian of the TAP03 model.
The model is named after the reference:
- - Miloushev V. Z. and Palmer A. (2005). R1rho relaxation for two-site
chemical exchange: General approximations and some exact solutions. J.
Magn. Reson., 177, 221-227. (U{DOI:
10.1016/j.jmr.2005.07.023<http://dx.doi.org/10.1016/j.jmr.2005.07.023>}).
+ - Trott, O., Abergel, D., and Palmer, A. (2003). An
average-magnetization analysis of R1rho relaxation outside of the fast
exchange. Mol. Phys., 101, 753â763. (U{DOI:
10.1080/0026897021000054826<http://dx.doi.org/10.1080/0026897021000054826>}).
-The code was copied from the TP02 model, hence it originates as the
funTrottPalmer.m Matlab file from the sim_all.tar file attached to task #7712
(https://gna.org/task/?7712). This is code from Nikolai Skrynnikov and
Martin Tollinger.
+The code was copied from the TP02 model (via the MP05 model), hence it
originates as the funTrottPalmer.m Matlab file from the sim_all.tar file
attached to task #7712 (https://gna.org/task/?7712). This is code from
Nikolai Skrynnikov and Martin Tollinger.
Links to the copyright licensing agreements from all authors are:
@@ -37,13 +37,13 @@
"""
# Python module imports.
-from math import atan, cos, pi, sin
+from math import atan, cos, pi, sin, sqrt
-def r1rho_MP05(r1rho_prime=None, omega=None, offset=None, pA=None, pB=None,
dw=None, kex=None, R1=0.0, spin_lock_fields=None, spin_lock_fields2=None,
back_calc=None, num_points=None):
+def r1rho_TAP03(r1rho_prime=None, omega=None, offset=None, pA=None, pB=None,
dw=None, kex=None, R1=0.0, spin_lock_fields=None, spin_lock_fields2=None,
back_calc=None, num_points=None):
"""Calculate the R1rho' values for the TP02 model.
- See the module docstring for details. This is the Miloushev and Palmer
(2005) equation according to Korzhnev (J. Biomol. NMR (2003), 26, 39-48).
+ See the module docstring for details. This is the Trott, Abergel and
Palmer (2003) equation.
@keyword r1rho_prime: The R1rho_prime parameter value (R1rho with
no exchange).
@@ -76,6 +76,9 @@
Wa = omega # Larmor frequency [s^-1].
Wb = omega + dw # Larmor frequency [s^-1].
kex2 = kex**2
+ W = pA*Wa + pB*Wb # Pop-averaged Larmor frequency [s^-1].
+ sigma = pB*Wa + pA*Wb
+ sigma2 = sigma**2
# The numerator.
phi_ex = pA * pB * dw**2
@@ -83,17 +86,19 @@
# Loop over the dispersion points, back calculating the R1rho values.
for i in range(num_points):
+ # The gamma factor.
+ gamma = 1.0 + phi_ex*(sigma2 - kex2 + spin_lock_fields2[i]) /
(sigma2 + kex2 + spin_lock_fields2[i])
+
# We assume that A resonates at 0 [s^-1], without loss of generality.
- W = pA*Wa + pB*Wb # Pop-averaged Larmor
frequency [s^-1].
da = Wa - offset[i] # Offset of spin-lock
from A.
db = Wb - offset[i] # Offset of spin-lock
from B.
d = W - offset[i] # Offset of spin-lock
from pop-average.
- waeff2 = spin_lock_fields2[i] + da**2 # Effective field at A.
- wbeff2 = spin_lock_fields2[i] + db**2 # Effective field at B.
- weff2 = spin_lock_fields2[i] + d**2 # Effective field at
pop-average.
+ waeff2 = spin_lock_fields2[i] + gamma*da**2 # Effective field at
A.
+ wbeff2 = spin_lock_fields2[i] + gamma*db**2 # Effective field at
B.
+ weff2 = spin_lock_fields2[i] + gamma*d**2 # Effective field at
pop-average.
# The rotating frame flip angle.
- theta = atan(spin_lock_fields[i] / d)
+ theta = atan(sqrt(gamma)*spin_lock_fields[i] / d)
# Repetitive calculations (to speed up calculations).
sin_theta2 = sin(theta)**2
@@ -106,9 +111,7 @@
continue
# Denominator.
- waeff2_wbeff2 = waeff2*wbeff2
- fact = 1.0 + 2.0*kex2*(pA*waeff2 + pB*wbeff2) / (waeff2_wbeff2 +
weff2*kex2)
- denom = waeff2_wbeff2/weff2 + kex2 - sin_theta2*phi_ex*(fact)
+ denom = waeff2*wbeff2/weff2 + kex2 - 2.0*sin_theta2*phi_ex*kex +
(1.0 - gamma)*spin_lock_fields2[i]
# Avoid divide by zero.
if denom == 0.0:
@@ -116,4 +119,4 @@
continue
# R1rho calculation.
- back_calc[i] = R1_cos_theta2 + R1rho_prime_sin_theta2 + sin_theta2 *
numer / denom
+ back_calc[i] = R1_cos_theta2 + R1rho_prime_sin_theta2 + sin_theta2 *
numer / denom / gamma
r21480 - in /branches/relax_disp/lib/dispersion: __init__.py tap03.py